No. ENCODE themselves admitted that their definition of “function” did not actually demonstrate meaningful biological function, in a paper they published in 2014:
The science is very clear on the matter: The large majority of the human genome is junk. The hype and publicity produced by ENCODE at the time it’s initial publication, however, did not reflect this. That is a failing of Public Relations and the communication of science to the public. It is not a reflection of the actual science.
Of course, if you do not take the time to actually understand the evidence, you will be left in the position of being confused by the “diversity of points of view” without being able to determine which points of view are correct.
No, not at all. There are many non-genic sequences with functions and there are many non-protein-coding sequences that are parts of genes. Not sure where you got that idea.
There is no such thing as “genes vs junk”. It’s “functional vs junk”. Some functional sequences are not part of genes. Now part of the confusion may have to do with the definition of “gene”. A protein-coding gene includes all the protein-coding bits but it also includes introns in between those bits and regulatory sequences both before and after those bits. Introns are mostly junk, and some other non-coding parts of genes are junk too. But the regulatory sequences are not junk. There are also lots of genes that are transcribed to RNA but not translated to protein. Those aren’t junk either. Then again, lots of junk is sometimes transcribed.
Note that a mutation in junk DNA can create a regulatory sequence where there shouldn’t be one, and that could create a deleterious “function” that reduces fitness.
Diseases like Alzheimer’s can be caused without much loss of function because it strikes the organism after the period where it is fruitful in reproductive terms…
Tell a guy with Alzheimer’s his disease is caused by meaningless changes to parts of the genome that have no function.
Ignorance mostly. My bad. I’m just trying to learn this stuff.
I guess that’s where I got tripped up. That’s kinda how I’d alway heard it - most of DNA was junk, the rest are the genes. It makes a lot more sense to me to think about “functional vs junk”.
OK, that clarifies things quite a bit. I thought that the regulatory sequences were junk too.
Should be a fair inference… it doesn’t have much impact on reproductive fitness.
Some of the population get it, others don’t. So a mutation being a cause is likely.
Hence it’s more likely that it involves a mutation that is not selected for or against.
Anyway, alzhiemers is just an example of important things which are more or less neutral with respect to reproductive success.
It isn’t a fair inference. Alzheimer’s could be due to a mutation in a functional gene that isn’t selected out of the population because it doesn’t impact reproductive fitness.
Several mutations/polymorphisms have been identified that are associated with Alzheimer’s. For example a polymorphism in APOE from a T to a C that changes a cysteine to an argenine residue in the protein product. Missense mutations in APP, PSEN1, and PSEN2 can also contribute.